MolNFT v1 · #79279 · protein
Glycogen phosphorylase B in complex with 3 -C-(hydroxymethyl)-beta-D- glucopyranonucleoside of 5-fluorouracil
3SYM · Glycogen phosphorylase, muscle form: “Glycogen phosphorylase B in complex with 3 -C-(hydroxymethyl)-beta-D- glucopyranonucleoside of 5-fluorouracil”. X-ray diffraction, 1 ligand (GP0), 12 pockets (best druggability 0.82). MolNFT v1…
- PDB
- 3SYM
- Type
- protein
- Length
- 807 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycogen phosphorylase, muscle form
- EC
- 2.4.1.1
- UniProt
- P00489
- Ligands
- GP0
- Pockets
- 12 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycogen phosphorylase, muscle form (EC 2.4.1.1) | protein | 807 | 53% helix, 16% strand | P00489 |
Ligands and binding sites
- GP0 · 5-fluoro-1-[3-C-(hydroxymethyl)-beta-D-glucopyranosyl]pyrimidine-2,4(1H,3H)-dione · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 192 | 0.82 | 0.96 | 40 | GP0 |
| 2 | 94 | 0.75 | 0.96 | 26 | empty |
| 3 | 302 | 0.68 | 0.83 | 36 | empty |
| 4 | 122 | 0.52 | 0.81 | 19 | empty |
| 5 | 222 | 0.51 | 0.76 | 20 | empty |
Modifications
Observed in the structure: 1 modified (cofactor).
Compared structures
- 3SYM · Glycogen Phosphorylase b in complex with 3 -C-(hydroxymethyl)-beta-D-glucopyranonucleoside… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P00489
- Elsewhere: RCSB PDB 3SYM · PDBe 3SYM · UniProt P00489
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